biocomputing

Could your next hard drive be made with DNA?

Okay, so maybe not your next one, but in a few year’s time? Maybe your storage will be writ across DNA itself. Researchers at Stanford have developed a method to store binary code on DNA. Dubbed the “recombinase addressable data (RAD) module,” the method controls the synthesis and degradation of two proteins, integrase and excisionase. With RAD, a particular section of a microbe’s DNA is tweaked to glow either red or green under ultraviolet light — and it can be switched back and forth at will.

What really sets this biological bit apart from others is that it can be reliably, and non-destructively, switched back and forth. It took the researchers three years to come up with the precise cocktail of proteins to achieve this feat. Since the switch is programmed into the microbes, it remains in its current state while the cell doubles, and can then be modified if needed.

“Programmable data storage within the DNA of living cells would seem an incredibly powerful tool for studying cancer, aging, organismal development and even the natural environment,” said synthetic biologist Drew Endy, but we’re a while from getting it to a more useful computational state. It’s currently got around a 30 minute switch time. As Endy put it, “We’re probably looking at a decade from when we started to get to a full byte.”

In the summer of 2013, I participated in the International Genetically Engineered Machine (iGEM) competition: an undergraduate research contest in the field of synthetic biology. My team and I created a biocomputing project, in which we exploited some natural properties of DNA and bacteria to find a large-scale probability-based solution to a Travelling Salesman Problem.

ACS Synthetic Biology, a journal dedicated to the field, offered to publish an article for any team that made it to the worldwide championships with a successful project – and here is ours.

Not all computers are made of silicon. By definition, a computer is anything that processes data, performs calculations, or uses so-called logic gates to turn inputs (for example, 1s and 0s in binary code) into outputs. And now, a small international community of scientists is working to expand the realm of computers to include cells, animals, and other living organisms. Some of their experiments are highly theoretical; others represent the first steps toward usable biological computers. All are attempts to make life perform work now done by chips and circuit boards.

Last year, for example, a computer scientist at the University of the West of England named Andy Adam­atzky and a team of Japanese researchers built logic gates that ran on soldier crabs. First they constructed mazes that replicated the shape of the wires in a computer’s logic gates.

Then they chased two swarms of crabs (inputs) from one end of the gate to the other. When the swarms collided, they combined to form a new swarm (output), which often headed in the direction of the sum of their vectors, demonstrating that a living, somewhat random system can produce useful order.

‘Biocomputer Music’ is a composition for piano and biocomputer. The biocomputer is an unprecedented musical machine built in my research laboratory at ICCMR (Plymouth University) based on programmable organisms cultured on circuit boards, and which are capable of growing their own circuits. This movie introduces the research behind this technology and the musical ideas that motivated the composition.